Objective: This study evaluated the effect of various endodontic irrigation regimens, using NaOCl followed by different agents for smear layer removal, on the surface and interface of Biodentine with dentine. Materials and methods: Furcal perforations were produced in 60 permanent mandibular molars. The walls of the perforated area were contaminated with blood and then perforations were covered with Biodentine and the teeth were divided into six groups (n = 10). In the control group, all irrigation procedures were performed using distilled water. In the other five groups 5.25% NaOCl was used as initial irrigant followed by: distilled water (DW group); 17% ethylenediaminetetraacetic acid (EDTA group); 37% phosphoric acid (PA group); 10% citric acid (CA group); and 7% maleic acid (MA group). The specimens were analysed using scanning electron microscopy (SEM) before and after the irrigation procedure to evaluate the morphology of Biodentine on the surface. SEM images were analysed qualitatively using a score system (Score 0, no modification between initial and final images; Score 1, modification between initial and final images). Push-out bond strength test was performed 7 days after sample preparation. Data were statistically analysed using Kruskal-Wallis and Dunn tests (P 0.05). Results: All irrigation regimens modified the topography of Biodentine. The regimens that used NaOCl/DW and NaOCl/EDTA showed significantly lower push-out bond strength values when compared to NaOCl/PA, NaOCl/CA, NaOCl/MA and control (P 0.05). Conclusions: The regimens using NaOCl/DW or NaOCl/EDTA compromised the push-out bond strength results when compared with other groups. Keywords: acids, Biodentine, blood contamination, chelating agent, furcal perforation repair